From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Nov 1 07:22:14 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 1 Nov 2014 12:22:14 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Geoff, I agree with your analysis, PhaseGatingImageFilter is not adequate for streaming, which is not surprising since Cyril uses it for iterative reconstruction and he typically works with the full stack of projections in RAM. I think there is a simple solution: move the update of the geometry from the GenerateData to the GenerateOutputInformation. That should solve the issue for you. Enclosed is a change suggestion, can you give it a try in the application you have built? I'll commit it if it helps, Simon On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > I?m trying to use the PhaseGatingImageFilter class to reconstruct a single > breathing phase volume and am running into some problems. I?ve incorporated > this class into an application similar to rtkfdk, putting it in the pipeline > between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If > I run the application trying to select a subset of projections using the > method SetGatingWindowCenter, I get a segmentation fault. The fault is > occurring due to allocation errors in > rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears > that since the geometry specific to the selected projections is selected in > PhaseGatingImageFilter::GenerateData, there is a disconnect between the > geometry size and projection stack size during GenerateInputRequestedRegion > in the pipeline (pipeline OutputInformation shows the projection stack size > is equal to the size of the selected breathing phase projections, but the > geometry size is still the total number of (unsorted) projections). > > I can workaround this problem by calling PhaseGatingImageFilter->Update(), > but I think this will break the streaming functionality? Any easy solutions > to this problem that will preserve streaming and let me run the full > pipeline with only one Update call? My guess is I will need to move the > geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() > then call UpdateOutputInformation in the main application? > > Thanks, > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkPhaseGatingImageFilter.txx Type: application/octet-stream Size: 9060 bytes Desc: not available URL: From gdhugo at vcu.edu Mon Nov 3 10:15:45 2014 From: gdhugo at vcu.edu (Geoff Hugo) Date: Mon, 3 Nov 2014 10:15:45 -0500 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Hi Simon, Yes, this was what I was thinking as well. Thanks for implementing it, it worked fine. Geoff ------------------------------------ Geoffrey D. Hugo, Ph.D. Associate Professor, Radiation Oncology Director, Medical Physics Graduate Program Virginia Commonwealth University (804) 628 3457 On Nov 1, 2014, at 7:22 AM, Simon Rit wrote: > Hi Geoff, > I agree with your analysis, PhaseGatingImageFilter is not adequate for > streaming, which is not surprising since Cyril uses it for iterative > reconstruction and he typically works with the full stack of > projections in RAM. I think there is a simple solution: move the > update of the geometry from the GenerateData to the > GenerateOutputInformation. That should solve the issue for you. > Enclosed is a change suggestion, can you give it a try in the > application you have built? > I'll commit it if it helps, > Simon > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a single >> breathing phase volume and am running into some problems. I?ve incorporated >> this class into an application similar to rtkfdk, putting it in the pipeline >> between ParkerShortScanImageFilter and FDKConeBeamReconstructionFilter. If >> I run the application trying to select a subset of projections using the >> method SetGatingWindowCenter, I get a segmentation fault. The fault is >> occurring due to allocation errors in >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It appears >> that since the geometry specific to the selected projections is selected in >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the >> geometry size and projection stack size during GenerateInputRequestedRegion >> in the pipeline (pipeline OutputInformation shows the projection stack size >> is equal to the size of the selected breathing phase projections, but the >> geometry size is still the total number of (unsorted) projections). >> >> I can workaround this problem by calling PhaseGatingImageFilter->Update(), >> but I think this will break the streaming functionality? Any easy solutions >> to this problem that will preserve streaming and let me run the full >> pipeline with only one Update call? My guess is I will need to move the >> geometry subselection to PhaseGatingImageFilter::GenerateOutputInformation() >> then call UpdateOutputInformation in the main application? >> >> Thanks, >> Geoff >> >> ------------------------------------ >> Geoffrey D. Hugo, Ph.D. >> Associate Professor, Radiation Oncology >> Director, Medical Physics Graduate Program >> Virginia Commonwealth University >> (804) 628 3457 >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > From simon.rit at creatis.insa-lyon.fr Mon Nov 3 12:15:15 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 3 Nov 2014 18:15:15 +0100 Subject: [Rtk-users] Issues using PhaseGatingImageFilter In-Reply-To: References: Message-ID: Great, it's been pushed . Simon On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo wrote: > Hi Simon, > > Yes, this was what I was thinking as well. Thanks for implementing it, it > worked fine. > > Geoff > > ------------------------------------ > Geoffrey D. Hugo, Ph.D. > Associate Professor, Radiation Oncology > Director, Medical Physics Graduate Program > Virginia Commonwealth University > (804) 628 3457 > > > On Nov 1, 2014, at 7:22 AM, Simon Rit > wrote: > > > Hi Geoff, > > I agree with your analysis, PhaseGatingImageFilter is not adequate for > > streaming, which is not surprising since Cyril uses it for iterative > > reconstruction and he typically works with the full stack of > > projections in RAM. I think there is a simple solution: move the > > update of the geometry from the GenerateData to the > > GenerateOutputInformation. That should solve the issue for you. > > Enclosed is a change suggestion, can you give it a try in the > > application you have built? > > I'll commit it if it helps, > > Simon > > > > On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo wrote: > >> I?m trying to use the PhaseGatingImageFilter class to reconstruct a > single > >> breathing phase volume and am running into some problems. I?ve > incorporated > >> this class into an application similar to rtkfdk, putting it in the > pipeline > >> between ParkerShortScanImageFilter and > FDKConeBeamReconstructionFilter. If > >> I run the application trying to select a subset of projections using the > >> method SetGatingWindowCenter, I get a segmentation fault. The fault is > >> occurring due to allocation errors in > >> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion. It > appears > >> that since the geometry specific to the selected projections is > selected in > >> PhaseGatingImageFilter::GenerateData, there is a disconnect between the > >> geometry size and projection stack size during > GenerateInputRequestedRegion > >> in the pipeline (pipeline OutputInformation shows the projection stack > size > >> is equal to the size of the selected breathing phase projections, but > the > >> geometry size is still the total number of (unsorted) projections). > >> > >> I can workaround this problem by calling > PhaseGatingImageFilter->Update(), > >> but I think this will break the streaming functionality? Any easy > solutions > >> to this problem that will preserve streaming and let me run the full > >> pipeline with only one Update call? My guess is I will need to move the > >> geometry subselection to > PhaseGatingImageFilter::GenerateOutputInformation() > >> then call UpdateOutputInformation in the main application? > >> > >> Thanks, > >> Geoff > >> > >> ------------------------------------ > >> Geoffrey D. Hugo, Ph.D. > >> Associate Professor, Radiation Oncology > >> Director, Medical Physics Graduate Program > >> Virginia Commonwealth University > >> (804) 628 3457 > >> > >> > >> > >> _______________________________________________ > >> Rtk-users mailing list > >> Rtk-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Tue Nov 4 10:48:47 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Tue, 4 Nov 2014 15:48:47 +0000 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK Message-ID: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Dear all, We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed image does not look as expected. The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); Please let me know if you have any ideas on what we might be doing wrong. Thank you for your help. Kind regards, Andria ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCCPM_TomoGeometry.pdf Type: application/pdf Size: 83384 bytes Desc: NCCPM_TomoGeometry.pdf URL: From ghostcz at hotmail.com Tue Nov 4 11:17:10 2014 From: ghostcz at hotmail.com (louie L) Date: Tue, 4 Nov 2014 17:17:10 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi Andria, Can you explain the setup with some more details? Which is the axis of rotation? I think if the isocenter is on the detector, the sid should be set equal to the sdd. Best regards, Louie Greetings from my iOS! > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote: > >> >> >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to reconstruct a digital breast tomosynthesis stack of projections acquired using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector remains stationary while the x-ray tube moves around a centre of rotation located at the detector (see attached diagram). The >> changes we made to FirstReconstruction.cxx so that it represents the Hologic Geometry are that the sdd and sourceOffesetY both vary as a function of the rotation of the source (sid*sin(angleTheta) >> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> Kind regards, >> Andria > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be accessed anywhere > > ******************************************************************************************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Tue Nov 4 11:55:06 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 4 Nov 2014 17:55:06 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Hi, When the source moves, along which axis of the detector is it? I would have expected it to move along the X axis. There is another option to set the geometry that might be easier for you, Reg23ProjectionGeometry . In any case, your scheme is wrong and I agree with Louie, you should think of the source parameters as the coordinates if all angles are set to 0 so in your case sdd==sid. Simon On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > Hi Andria, > > Can you explain the setup with some more details? Which is the axis of > rotation? > I think if the isocenter is on the detector, the sid should be set equal > to the sdd. > > Best regards, > Louie > > Greetings from my iOS! > > On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY > HOSPITAL NHS FOUNDATION TRUST) wrote: > > > Dear all, > > We used the FirstReconstruction.cxx code with minor changes to reconstruct > a digital breast tomosynthesis stack of projections acquired using a > Hologic Selenia Dimenions system. Unfortunately, the reconstructed image > does not look as expected. > > The characteristics of the geometry of the system are that the detector > remains stationary while the x-ray tube moves around a centre of rotation > located at the detector (see attached diagram). The changes we made to > FirstReconstruction.cxx so that it represents the Hologic Geometry are that > the sdd and sourceOffesetY both vary as a function of the rotation of the > source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in > all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our > geometry definition is: > > geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); > > Please let me know if you have any ideas on what we might be doing wrong. > > > Thank you for your help. > > Kind regards, > > Andria > > > > > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or > take any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS > staff in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > > > ******************************************************************************************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 4 12:08:11 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 4 Nov 2014 18:08:11 +0100 Subject: [Rtk-users] Tomosynthesis Reconstruction using RTK In-Reply-To: References: <20141104155115.C299A448D67@nhs-pd1e-esg101.ad1.nhs.net> Message-ID: Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing may be the projection shift (-isox,0). If the input projection are plain images from a real system without origin definition in its format, then the projection shift may be (0,-isoy) instead, with projection origin at the corner pixel. 2014-11-04 17:55 GMT+01:00 Simon Rit : > Hi, > When the source moves, along which axis of the detector is it? I would > have expected it to move along the X axis. > There is another option to set the geometry that might be easier for you, > Reg23ProjectionGeometry > . > In any case, your scheme is wrong and I agree with Louie, you should think > of the source parameters as the coordinates if all angles are set to 0 so > in your case sdd==sid. > Simon > > On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >> reconstruct a digital breast tomosynthesis stack of projections acquired >> using a Hologic Selenia Dimenions system. Unfortunately, the reconstructed >> image does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are that >> the sdd and sourceOffesetY both vary as a function of the rotation of the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >> wrong. >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> ******************************************************************************************************************** >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> ******************************************************************************************************************** >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andria.hadjipanteli at nhs.net Thu Nov 6 10:32:53 2014 From: andria.hadjipanteli at nhs.net (Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST)) Date: Thu, 6 Nov 2014 15:32:53 +0000 Subject: [Rtk-users] Rtk-users Digest, Vol 27, Issue 3 In-Reply-To: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> References: <20141104171026.76ECE45892C@nhs-pd1e-esg004.ad1.nhs.net> Message-ID: <20141106153516.B4953449A11@nhs-pd1e-esg109.ad1.nhs.net> Dear Louie/Simon/Chao, Thanks a lot for your help. Your suggestions have been useful. Kind regards, Andria On 04/11/2014 17:09, "rtk-users-request at public.kitware.com" wrote: >Warning: This message contains unverified links which may not be safe. >You should only click links if you are sure they are from a trusted >source. >Send Rtk-users mailing list submissions to > rtk-users at public.kitware.com > >To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/rtk-users >or, via email, send a message with subject or body 'help' to > rtk-users-request at public.kitware.com > >You can reach the person managing the list at > rtk-users-owner at public.kitware.com > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Rtk-users digest..." > > >Today's Topics: > > 1. Re: Tomosynthesis Reconstruction using RTK (louie L) > 2. Re: Tomosynthesis Reconstruction using RTK (Simon Rit) > 3. Re: Tomosynthesis Reconstruction using RTK (Chao Wu) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 4 Nov 2014 17:17:10 +0100 >From: louie L >To: "Hadjipanteli Andria (ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST)" >Cc: "rtk-users at public.kitware.com" >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi Andria, > >Can you explain the setup with some more details? Which is the axis of >rotation? >I think if the isocenter is on the detector, the sid should be set equal >to the sdd. > >Best regards, >Louie > >Greetings from my iOS! > >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>HOSPITAL NHS FOUNDATION TRUST) wrote: >> >>> >>> >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>>reconstruct a digital breast tomosynthesis stack of projections >>>acquired using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the >>>detector remains stationary while the x-ray tube moves around a centre >>>of rotation located at the detector (see attached diagram). The >>> changes we made to FirstReconstruction.cxx so that it represents the >>>Hologic Geometry are that the sdd and sourceOffesetY both vary as a >>>function of the rotation of the source (sid*sin(angleTheta) >>> and sid*cos(angleTheta) respectively) while in all cases gantryAngle= >>>0, sid = 700 mm and isox = -detectorWidth/2. Our geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> Kind regards, >>> Andria >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >>intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail >>or take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >>staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >>information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >>accessed anywhere >> >> >>************************************************************************* >>******************************************* >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >36/attachment-0001.html> >-------------- next part -------------- >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > >------------------------------ > >Message: 2 >Date: Tue, 4 Nov 2014 17:55:06 +0100 >From: Simon Rit >To: louie L >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Hi, >When the source moves, along which axis of the detector is it? I would >have >expected it to move along the X axis. >There is another option to set the geometry that might be easier for you, >Reg23ProjectionGeometry >. >In any case, your scheme is wrong and I agree with Louie, you should think >of the source parameters as the coordinates if all angles are set to 0 so >in your case sdd==sid. >Simon > >On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: > >> Hi Andria, >> >> Can you explain the setup with some more details? Which is the axis of >> rotation? >> I think if the isocenter is on the detector, the sid should be set equal >> to the sdd. >> >> Best regards, >> Louie >> >> Greetings from my iOS! >> >> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >> HOSPITAL NHS FOUNDATION TRUST) wrote: >> >> >> Dear all, >> >> We used the FirstReconstruction.cxx code with minor changes to >>reconstruct >> a digital breast tomosynthesis stack of projections acquired using a >> Hologic Selenia Dimenions system. Unfortunately, the reconstructed image >> does not look as expected. >> >> The characteristics of the geometry of the system are that the detector >> remains stationary while the x-ray tube moves around a centre of >>rotation >> located at the detector (see attached diagram). The changes we made to >> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>that >> the sdd and sourceOffesetY both vary as a function of the rotation of >>the >> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) while >>in >> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >> geometry definition is: >> >> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >> >> Please let me know if you have any ideas on what we might be doing >>wrong. >> >> >> Thank you for your help. >> >> Kind regards, >> >> Andria >> >> >> >> >> >> >> >>************************************************************************* >>******************************************* >> >> This message may contain confidential information. If you are not the >> intended recipient please inform the >> sender that you have received the message in error before deleting it. >> Please do not disclose, copy or distribute information in this e-mail or >> take any action in reliance on its contents: >> to do so is strictly prohibited and may be unlawful. >> >> Thank you for your co-operation. >> >> NHSmail is the secure email and directory service available for all NHS >> staff in England and Scotland >> NHSmail is approved for exchanging patient data and other sensitive >> information with NHSmail and GSi recipients >> NHSmail provides an email address for your career in the NHS and can be >> accessed anywhere >> >> >> >>************************************************************************* >>******************************************* >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >45/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Tue, 4 Nov 2014 18:08:11 +0100 >From: Chao Wu >To: Simon Rit >Cc: "Hadjipanteli Andria \(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION > TRUST\)" , "rtk-users at public.kitware.com" > >Subject: Re: [Rtk-users] Tomosynthesis Reconstruction using RTK >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Agree, sdd==sid=700*cos(theta_in_the_picture). Another suspicious thing >may >be the projection shift (-isox,0). If the input projection are plain >images >from a real system without origin definition in its format, then the >projection shift may be (0,-isoy) instead, with projection origin at the >corner pixel. > >2014-11-04 17:55 GMT+01:00 Simon Rit : > >> Hi, >> When the source moves, along which axis of the detector is it? I would >> have expected it to move along the X axis. >> There is another option to set the geometry that might be easier for >>you, >> Reg23ProjectionGeometry >> >> >>. >> In any case, your scheme is wrong and I agree with Louie, you should >>think >> of the source parameters as the coordinates if all angles are set to 0 >>so >> in your case sdd==sid. >> Simon >> >> On Tue, Nov 4, 2014 at 5:17 PM, louie L wrote: >> >>> Hi Andria, >>> >>> Can you explain the setup with some more details? Which is the axis of >>> rotation? >>> I think if the isocenter is on the detector, the sid should be set >>>equal >>> to the sdd. >>> >>> Best regards, >>> Louie >>> >>> Greetings from my iOS! >>> >>> On 04 Nov 2014, at 17:04, Hadjipanteli Andria (ROYAL SURREY COUNTY >>> HOSPITAL NHS FOUNDATION TRUST) wrote: >>> >>> >>> Dear all, >>> >>> We used the FirstReconstruction.cxx code with minor changes to >>> reconstruct a digital breast tomosynthesis stack of projections >>>acquired >>> using a Hologic Selenia Dimenions system. Unfortunately, the >>>reconstructed >>> image does not look as expected. >>> >>> The characteristics of the geometry of the system are that the detector >>> remains stationary while the x-ray tube moves around a centre of >>>rotation >>> located at the detector (see attached diagram). The changes we made to >>> FirstReconstruction.cxx so that it represents the Hologic Geometry are >>>that >>> the sdd and sourceOffesetY both vary as a function of the rotation of >>>the >>> source (sid*sin(angleTheta) and sid*cos(angleTheta) respectively) >>>while in >>> all cases gantryAngle= 0, sid = 700 mm and isox = -detectorWidth/2. Our >>> geometry definition is: >>> >>> geometry->AddProjection(700,sdd,0,-isox,0,0,0,0,sourceOffsetY); >>> >>> Please let me know if you have any ideas on what we might be doing >>> wrong. >>> >>> Thank you for your help. >>> >>> Kind regards, >>> >>> Andria >>> >>> >>> >>> >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> This message may contain confidential information. If you are not the >>> intended recipient please inform the >>> sender that you have received the message in error before deleting it. >>> Please do not disclose, copy or distribute information in this e-mail >>>or >>> take any action in reliance on its contents: >>> to do so is strictly prohibited and may be unlawful. >>> >>> Thank you for your co-operation. >>> >>> NHSmail is the secure email and directory service available for all NHS >>> staff in England and Scotland >>> NHSmail is approved for exchanging patient data and other sensitive >>> information with NHSmail and GSi recipients >>> NHSmail provides an email address for your career in the NHS and can be >>> accessed anywhere >>> >>> >>> >>>************************************************************************ >>>******************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >ef/attachment.html> > >------------------------------ > >Subject: Digest Footer > >_______________________________________________ >Rtk-users mailing list >Rtk-users at public.kitware.com >http://public.kitware.com/mailman/listinfo/rtk-users > > >------------------------------ > >End of Rtk-users Digest, Vol 27, Issue 3 >**************************************** > ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** From theday79 at gmail.com Mon Nov 10 17:37:08 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Mon, 10 Nov 2014 17:37:08 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Message-ID: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Hi all, I've been successfully using "ElektaSynergyGeometryReader" class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I'm wondering if some of you are also "suffering" from this upgrade or having any ideas about this issue. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 11 03:24:22 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 11 Nov 2014 09:24:22 +0100 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: <000f01cffd36$dd6db6d0$98492470$@gmail.com> References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park wrote: > Hi all, > > > > I?ve been successfully using ?ElektaSynergyGeometryReader? class to > extract the CBCT geometry from our Elekta database files (IMAGE.DBF and > FRAME.DBF). > > > > Recently, our Elekta XVI systems are under upgrade and I found that this > latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, > there seems to be some .sql files that contains those geometry information. > > > > I?m wondering if some of you are also ?suffering? from this upgrade or > having any ideas about this issue. > > > > Thanks. > > > > Yang > > > > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Tue Nov 11 10:53:17 2014 From: theday79 at gmail.com (Yang Kyun Park) Date: Tue, 11 Nov 2014 10:53:17 -0500 Subject: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files In-Reply-To: References: <000f01cffd36$dd6db6d0$98492470$@gmail.com> Message-ID: <001e01cffdc7$9cebebe0$d6c3c3a0$@gmail.com> Hi Simon, I feel some responsibilities for it if I?m the first user/reporter of the new XVI system. Let me try to figure it out. Thanks. Yang From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: Tuesday, November 11, 2014 3:24 AM To: Yang Kyun Park Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] New version of Eletka XVI software (5.0.2) no longer uses .DBF files Hi Yang, I knew this was coming but you are the first one to report it to me. This is actually good news because the DBF reader was far from efficient and SQL is easier. Would you be willing to try to develop a new reader? I'm sure there are many portable SQL readers that could help us. Simon On Mon, Nov 10, 2014 at 11:37 PM, Yang Kyun Park > wrote: Hi all, I?ve been successfully using ?ElektaSynergyGeometryReader? class to extract the CBCT geometry from our Elekta database files (IMAGE.DBF and FRAME.DBF). Recently, our Elekta XVI systems are under upgrade and I found that this latest version of XVI (v 5.0.2) no longer uses those DBF files. Instead, there seems to be some .sql files that contains those geometry information. I?m wondering if some of you are also ?suffering? from this upgrade or having any ideas about this issue. Thanks. Yang _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 09:09:02 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 17:09:02 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Thanks *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 16:46 GMT+03:00 Guangming Zang : > Hi, > I am using the sart reconstruction in RTK, it works well.Thanks for your > great work. > and i was wondering do you have any plan to add other filters except > Joseph, such as Kaiser-Bessel??? ( described here > http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) > BTW, i have read the messages sent by other users( > http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) > but i still can not make it. can u help me and explain again about using a > series of .tiff images ans sart algorithms to get the volume. > Thanks in advance > Best > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:09:31 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:09:31 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Guangming, To reconstruct a volume from a series of tiff files you have to let the algorithm know the geometrical relationship among the source, the volume and the projections stored in the tiffs. The idea is the same: RTK uses projection matrices and image coordinates to understand the positioning of those projections. The projection matrices are based on a lot of geometrical parameters like gantry angle, source position, detector position, in-plane and out-of-plane rotation angles of the detector etc. I won't go though all since most of them have no differences if you use tiff files or whatever format as input. I focus on some tiff tips. In the simplest situation, the tiff files contain correct resolution (DPI) information, then you need to do nothing on these files. You have to specify the correct detector offset though, since in the tiff image coordinates the origin is the first pixel (corner pixel) which is apparently not the intersection of the central ray and the detector. The detector offsets in x and y actually mean the position of the image origin (the first pixel) in the coordinate system centred at the intersection. Since the direction cosines is an identity matrix and pixel sizes are positive, the detector offsets in x and y will be negative. If the resolution information of the tiff files is not correct, you have to rewrite this information. You can of course perform a pre-processing to change the DPI of all tiff files with a third-party software, or you can alter the RTK code to allow such changes after reading the images, by using a itk::ChangeInformationImageFilter filter. Another non-geometrical issue with tiff files is that when their integer pixel values are converted into attenuation, the maximum possible integer is used as the reference value. This may not be correct in practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no attenuation) leaving the integer range from 62001 to 65535 for statistical fluctuation. If for instance you only use the lower 14 bits for your data then this problem is more severe. For sure you can correct this by changing the code and specify the correct reference value. Hope these can help. Regards, Chao 2014-11-18 15:09 GMT+01:00 Guangming Zang : > Thanks > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 16:46 GMT+03:00 Guangming Zang : > >> Hi, >> I am using the sart reconstruction in RTK, it works well.Thanks for your >> great work. >> and i was wondering do you have any plan to add other filters except >> Joseph, such as Kaiser-Bessel??? ( described here >> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >> BTW, i have read the messages sent by other users( >> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >> but i still can not make it. can u help me and explain again about using >> a series of .tiff images ans sart algorithms to get the volume. >> Thanks in advance >> Best >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:36:52 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, About your other question, there is no plan to add Kaiser-Bessel basis functions that I'm aware of. But I would strongly encourage you to give it a try! Good luck with your project, Simon On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:43:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:43:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Chao, Thanks very much for your prompt and so kind reply. I will recheck the process of setting carefully with your suggestions and a short report may be given later. BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel or Trilinear)?? Thanks for your time. Regards Guangming 2014-11-18 19:09 GMT+03:00 Chao Wu : > Hi Guangming, > > To reconstruct a volume from a series of tiff files you have to let the > algorithm know the geometrical relationship among the source, the volume > and the projections stored in the tiffs. The idea is the same: RTK uses > projection matrices and image coordinates to understand the positioning of > those projections. The projection matrices are based on a lot of > geometrical parameters like gantry angle, source position, detector > position, in-plane and out-of-plane rotation angles of the detector etc. I > won't go though all since most of them have no differences if you use tiff > files or whatever format as input. I focus on some tiff tips. > > In the simplest situation, the tiff files contain correct resolution (DPI) > information, then you need to do nothing on these files. You have to > specify the correct detector offset though, since in the tiff image > coordinates the origin is the first pixel (corner pixel) which is > apparently not the intersection of the central ray and the detector. The > detector offsets in x and y actually mean the position of the image origin > (the first pixel) in the coordinate system centred at the intersection. > Since the direction cosines is an identity matrix and pixel sizes are > positive, the detector offsets in x and y will be negative. > > If the resolution information of the tiff files is not correct, you have > to rewrite this information. You can of course perform a pre-processing to > change the DPI of all tiff files with a third-party software, or you can > alter the RTK code to allow such changes after reading the images, by using > a itk::ChangeInformationImageFilter filter. > > Another non-geometrical issue with tiff files is that when their integer > pixel values are converted into attenuation, the maximum possible integer > is used as the reference value. This may not be correct in practice, e.g. > in your 16-bit tiffs you use 62000 to represent air (no attenuation) > leaving the integer range from 62001 to 65535 for statistical fluctuation. > If for instance you only use the lower 14 bits for your data then this > problem is more severe. For sure you can correct this by changing the code > and specify the correct reference value. > > Hope these can help. > > Regards, > Chao > > 2014-11-18 15:09 GMT+01:00 Guangming Zang : > >> Thanks >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >> >>> Hi, >>> I am using the sart reconstruction in RTK, it works well.Thanks for your >>> great work. >>> and i was wondering do you have any plan to add other filters except >>> Joseph, such as Kaiser-Bessel??? ( described here >>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>> BTW, i have read the messages sent by other users( >>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>> but i still can not make it. can u help me and explain again about using >>> a series of .tiff images ans sart algorithms to get the volume. >>> Thanks in advance >>> Best >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:46:39 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:46:39 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi Simon and Chao. Thanks , i see. :) Yeah, i am working on other basis functions now, maybe i can make a little contribution to our community in a later time. :) Thanks again for your guys's great work and valuable time. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:36 GMT+03:00 Simon Rit : > Hi, > About your other question, there is no plan to add Kaiser-Bessel basis > functions that I'm aware of. But I would strongly encourage you to give it > a try! > Good luck with your project, > Simon > > On Tue, Nov 18, 2014 at 5:09 PM, Chao Wu wrote: > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Tue Nov 18 11:47:16 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Tue, 18 Nov 2014 17:47:16 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: No, at the moment I mainly work on FDK. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?18? 5:43 PM? "Guangming Zang" ??? > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Nov 18 11:47:26 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 18 Nov 2014 17:47:26 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: The trilinear version is available with CUDA: http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html Simon On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang wrote: > Hi Chao, > Thanks very much for your prompt and so kind reply. > I will recheck the process of setting carefully with your suggestions and > a short report may be given later. > BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel > or Trilinear)?? > Thanks for your time. > Regards > Guangming > > > > 2014-11-18 19:09 GMT+03:00 Chao Wu : > >> Hi Guangming, >> >> To reconstruct a volume from a series of tiff files you have to let the >> algorithm know the geometrical relationship among the source, the volume >> and the projections stored in the tiffs. The idea is the same: RTK uses >> projection matrices and image coordinates to understand the positioning of >> those projections. The projection matrices are based on a lot of >> geometrical parameters like gantry angle, source position, detector >> position, in-plane and out-of-plane rotation angles of the detector etc. I >> won't go though all since most of them have no differences if you use tiff >> files or whatever format as input. I focus on some tiff tips. >> >> In the simplest situation, the tiff files contain correct resolution >> (DPI) information, then you need to do nothing on these files. You have to >> specify the correct detector offset though, since in the tiff image >> coordinates the origin is the first pixel (corner pixel) which is >> apparently not the intersection of the central ray and the detector. The >> detector offsets in x and y actually mean the position of the image origin >> (the first pixel) in the coordinate system centred at the intersection. >> Since the direction cosines is an identity matrix and pixel sizes are >> positive, the detector offsets in x and y will be negative. >> >> If the resolution information of the tiff files is not correct, you have >> to rewrite this information. You can of course perform a pre-processing to >> change the DPI of all tiff files with a third-party software, or you can >> alter the RTK code to allow such changes after reading the images, by using >> a itk::ChangeInformationImageFilter filter. >> >> Another non-geometrical issue with tiff files is that when their integer >> pixel values are converted into attenuation, the maximum possible integer >> is used as the reference value. This may not be correct in practice, e.g. >> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >> leaving the integer range from 62001 to 65535 for statistical fluctuation. >> If for instance you only use the lower 14 bits for your data then this >> problem is more severe. For sure you can correct this by changing the code >> and specify the correct reference value. >> >> Hope these can help. >> >> Regards, >> Chao >> >> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >> >>> Thanks >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 16:46 GMT+03:00 Guangming Zang : >>> >>>> Hi, >>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>> your great work. >>>> and i was wondering do you have any plan to add other filters except >>>> Joseph, such as Kaiser-Bessel??? ( described here >>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>> BTW, i have read the messages sent by other users( >>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html) >>>> but i still can not make it. can u help me and explain again about >>>> using a series of .tiff images ans sart algorithms to get the volume. >>>> Thanks in advance >>>> Best >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Tue Nov 18 11:49:51 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Tue, 18 Nov 2014 19:49:51 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Oh, I did not notice that. Thanks for pointing out. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:26:17 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:26:17 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi,Simon and Chao, i want to test the cuda performance in SART algorithm. but when i looked in the parameters in forwardprojection and backprojection. i got the enum: enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; So if i want to use the trilinear intrtpolation forwardprojection you mentioned , how should i set the -b and -p in SART? or how to choose -b and -p that i can get a fastest reconstruction in SART in this case?? thanks for your help in advance. Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-18 19:47 GMT+03:00 Simon Rit : > The trilinear version is available with CUDA: > > http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html > Simon > > On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Chao, >> Thanks very much for your prompt and so kind reply. >> I will recheck the process of setting carefully with your suggestions and >> a short report may be given later. >> BTW, do you have any plan recently to add other interpolation filter(e.g.Kaiser-Bessel >> or Trilinear)?? >> Thanks for your time. >> Regards >> Guangming >> >> >> >> 2014-11-18 19:09 GMT+03:00 Chao Wu : >> >>> Hi Guangming, >>> >>> To reconstruct a volume from a series of tiff files you have to let the >>> algorithm know the geometrical relationship among the source, the volume >>> and the projections stored in the tiffs. The idea is the same: RTK uses >>> projection matrices and image coordinates to understand the positioning of >>> those projections. The projection matrices are based on a lot of >>> geometrical parameters like gantry angle, source position, detector >>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>> won't go though all since most of them have no differences if you use tiff >>> files or whatever format as input. I focus on some tiff tips. >>> >>> In the simplest situation, the tiff files contain correct resolution >>> (DPI) information, then you need to do nothing on these files. You have to >>> specify the correct detector offset though, since in the tiff image >>> coordinates the origin is the first pixel (corner pixel) which is >>> apparently not the intersection of the central ray and the detector. The >>> detector offsets in x and y actually mean the position of the image origin >>> (the first pixel) in the coordinate system centred at the intersection. >>> Since the direction cosines is an identity matrix and pixel sizes are >>> positive, the detector offsets in x and y will be negative. >>> >>> If the resolution information of the tiff files is not correct, you have >>> to rewrite this information. You can of course perform a pre-processing to >>> change the DPI of all tiff files with a third-party software, or you can >>> alter the RTK code to allow such changes after reading the images, by using >>> a itk::ChangeInformationImageFilter filter. >>> >>> Another non-geometrical issue with tiff files is that when their integer >>> pixel values are converted into attenuation, the maximum possible integer >>> is used as the reference value. This may not be correct in practice, e.g. >>> in your 16-bit tiffs you use 62000 to represent air (no attenuation) >>> leaving the integer range from 62001 to 65535 for statistical fluctuation. >>> If for instance you only use the lower 14 bits for your data then this >>> problem is more severe. For sure you can correct this by changing the code >>> and specify the correct reference value. >>> >>> Hope these can help. >>> >>> Regards, >>> Chao >>> >>> 2014-11-18 15:09 GMT+01:00 Guangming Zang : >>> >>>> Thanks >>>> >>>> *Guangming Zang (Alex)* >>>> *King Abdullah University of Science and Technology(KAUST)* >>>> *University of Chinese Academy of Sciences(UCAS)* >>>> >>>> >>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> : >>>> >>>>> Hi, >>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>> your great work. >>>>> and i was wondering do you have any plan to add other filters except >>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>> BTW, i have read the messages sent by other users( >>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>> ) >>>>> but i still can not make it. can u help me and explain again about >>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>> Thanks in advance >>>>> Best >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:35:27 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:35:27 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: By the way,here is the test command and performance respectively:(the simulated data is same with the RayBoxIntersection in wiki) rtksimulatedgeometry -n 360 -o geometry.xml rtkdrawgeometricphantom -o box.mha --spacing 1 --dimension 90 --phantomfile box.txt rtksart -g geometry.xml -f CudaRayCast -b 2 -t 1 -p . -r rayboxintersection.mha -o cuda_sart.mha --spacing 1 --dimension 256 finally: rtkrayboxintersection -g geometry.xml -i box.mha -o rayboxintersection.mha --spacing 1 --dimension 256 OUTPUT: Main Starts............................ SART reconstruction Starts............................ Recording elapsed time... TRY_AND_EXIT_ON_ITK_EXCEPTION Starts............................ TRY_AND_EXIT_ON_ITK_EXCEPTION ends............................ SARTConeBeamReconstructionFilter timing: Extraction of projection sub-stacks: 13.0585 s Multiplication by zero: 4.37428 s Forward projection: 64.1553 s Subtraction: 5.54071 s Multiplication by lambda: 4.32212 s Ray box intersection: 19.6573 s Division: 4.55492 s Multiplication by the gating weights: 0 s Displaced detector: 3.96396 s Back projection: 1811.42 s It took... 1933.49 s Write is over,finished!............................ So can i use other -b and -p setting to make it faster currently?? Best Guangming 2014-11-19 16:26 GMT+03:00 Guangming Zang : > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 08:40:58 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 14:40:58 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Hi, I think you are looking at the code generated by gengetopt for the rtksart application. In general, it's simpler to simply do "rtksart --help" when you want to find out how to use a parameter. You will then find the following help section Projectors: -f, --fp=ENUM Forward projection method (possible values="Joseph", "RayCastInterpolator", "CudaRayCast" default=`Joseph') -b, --bp=ENUM Back projection method (possible values="VoxelBasedBackProjection", "Joseph", "CudaVoxelBased", "NormalizedJoseph" default=`VoxelBasedBackProjection') That should answer your question rtksart -b CudaVoxelBased. -p is the option for the path where the program will look for your projection images. Simon On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang wrote: > Hi,Simon and Chao, > i want to test the cuda performance in SART algorithm. > but when i looked in the parameters in forwardprojection and > backprojection. i got the enum: > > enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, > fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; > enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, > bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; > > So if i want to use the trilinear intrtpolation forwardprojection you > mentioned , how should i set the -b and -p in SART? or how to choose -b and > -p that i can get a fastest reconstruction in SART in this case?? > > thanks for your help in advance. > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-18 19:47 GMT+03:00 Simon Rit : > >> The trilinear version is available with CUDA: >> >> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >> Simon >> >> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi Chao, >>> Thanks very much for your prompt and so kind reply. >>> I will recheck the process of setting carefully with your suggestions >>> and a short report may be given later. >>> BTW, do you have any plan recently to add other interpolation >>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>> Thanks for your time. >>> Regards >>> Guangming >>> >>> >>> >>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>> >>>> Hi Guangming, >>>> >>>> To reconstruct a volume from a series of tiff files you have to let the >>>> algorithm know the geometrical relationship among the source, the volume >>>> and the projections stored in the tiffs. The idea is the same: RTK uses >>>> projection matrices and image coordinates to understand the positioning of >>>> those projections. The projection matrices are based on a lot of >>>> geometrical parameters like gantry angle, source position, detector >>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>> won't go though all since most of them have no differences if you use tiff >>>> files or whatever format as input. I focus on some tiff tips. >>>> >>>> In the simplest situation, the tiff files contain correct resolution >>>> (DPI) information, then you need to do nothing on these files. You have to >>>> specify the correct detector offset though, since in the tiff image >>>> coordinates the origin is the first pixel (corner pixel) which is >>>> apparently not the intersection of the central ray and the detector. The >>>> detector offsets in x and y actually mean the position of the image origin >>>> (the first pixel) in the coordinate system centred at the intersection. >>>> Since the direction cosines is an identity matrix and pixel sizes are >>>> positive, the detector offsets in x and y will be negative. >>>> >>>> If the resolution information of the tiff files is not correct, you >>>> have to rewrite this information. You can of course perform a >>>> pre-processing to change the DPI of all tiff files with a third-party >>>> software, or you can alter the RTK code to allow such changes after reading >>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>> >>>> Another non-geometrical issue with tiff files is that when their >>>> integer pixel values are converted into attenuation, the maximum possible >>>> integer is used as the reference value. This may not be correct in >>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>> then this problem is more severe. For sure you can correct this by changing >>>> the code and specify the correct reference value. >>>> >>>> Hope these can help. >>>> >>>> Regards, >>>> Chao >>>> >>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> : >>>> >>>>> Thanks >>>>> >>>>> *Guangming Zang (Alex)* >>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>> >>>>> >>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang >>>> >: >>>>> >>>>>> Hi, >>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>> your great work. >>>>>> and i was wondering do you have any plan to add other filters except >>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>> BTW, i have read the messages sent by other users( >>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>> ) >>>>>> but i still can not make it. can u help me and explain again about >>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>> Thanks in advance >>>>>> Best >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Wed Nov 19 08:50:48 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 19 Nov 2014 16:50:48 +0300 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes, thanks for your prompt reply. what i want is to figure out how to set -f and -b to get i fastest reconstruction (not -p,sorry for my mistake.). and in -b. which one is related to our trilinear interpolation, CudaRayCast?? thanks Best *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-19 16:40 GMT+03:00 Simon Rit : > Hi, > I think you are looking at the code generated by gengetopt for the rtksart > application. In general, it's simpler to simply do "rtksart --help" when > you want to find out how to use a parameter. You will then find the > following help section > Projectors: > -f, --fp=ENUM Forward projection method (possible > values="Joseph", "RayCastInterpolator", > "CudaRayCast" default=`Joseph') > -b, --bp=ENUM Back projection method (possible > values="VoxelBasedBackProjection", "Joseph", > "CudaVoxelBased", "NormalizedJoseph" > default=`VoxelBasedBackProjection') > That should answer your question rtksart -b CudaVoxelBased. -p is the > option for the path where the program will look for your projection images. > Simon > > On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi,Simon and Chao, >> i want to test the cuda performance in SART algorithm. >> but when i looked in the parameters in forwardprojection and >> backprojection. i got the enum: >> >> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >> >> So if i want to use the trilinear intrtpolation forwardprojection you >> mentioned , how should i set the -b and -p in SART? or how to choose -b and >> -p that i can get a fastest reconstruction in SART in this case?? >> >> thanks for your help in advance. >> Best >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-18 19:47 GMT+03:00 Simon Rit : >> >>> The trilinear version is available with CUDA: >>> >>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>> Simon >>> >>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>> guangming.zang at kaust.edu.sa> wrote: >>> >>>> Hi Chao, >>>> Thanks very much for your prompt and so kind reply. >>>> I will recheck the process of setting carefully with your suggestions >>>> and a short report may be given later. >>>> BTW, do you have any plan recently to add other interpolation >>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>> Thanks for your time. >>>> Regards >>>> Guangming >>>> >>>> >>>> >>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>> >>>>> Hi Guangming, >>>>> >>>>> To reconstruct a volume from a series of tiff files you have to let >>>>> the algorithm know the geometrical relationship among the source, the >>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>> uses projection matrices and image coordinates to understand the >>>>> positioning of those projections. The projection matrices are based on a >>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>> won't go though all since most of them have no differences if you use tiff >>>>> files or whatever format as input. I focus on some tiff tips. >>>>> >>>>> In the simplest situation, the tiff files contain correct resolution >>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>> specify the correct detector offset though, since in the tiff image >>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>> apparently not the intersection of the central ray and the detector. The >>>>> detector offsets in x and y actually mean the position of the image origin >>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>> positive, the detector offsets in x and y will be negative. >>>>> >>>>> If the resolution information of the tiff files is not correct, you >>>>> have to rewrite this information. You can of course perform a >>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>> software, or you can alter the RTK code to allow such changes after reading >>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>> >>>>> Another non-geometrical issue with tiff files is that when their >>>>> integer pixel values are converted into attenuation, the maximum possible >>>>> integer is used as the reference value. This may not be correct in >>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>> then this problem is more severe. For sure you can correct this by changing >>>>> the code and specify the correct reference value. >>>>> >>>>> Hope these can help. >>>>> >>>>> Regards, >>>>> Chao >>>>> >>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang >>>> >: >>>>> >>>>>> Thanks >>>>>> >>>>>> *Guangming Zang (Alex)* >>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>> >>>>>> >>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Hi, >>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>> your great work. >>>>>>> and i was wondering do you have any plan to add other filters except >>>>>>> Joseph, such as Kaiser-Bessel??? ( described here >>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>> BTW, i have read the messages sent by other users( >>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>> ) >>>>>>> but i still can not make it. can u help me and explain again about >>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>> Thanks in advance >>>>>>> Best >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> This message and its contents, including attachments are intended >>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>> have received this message in error, please notify me immediately and >>>>>> delete this message from your computer system. Any unauthorized use or >>>>>> distribution is prohibited. Please consider the environment before printing >>>>>> this email. >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Nov 19 09:02:25 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 19 Nov 2014 15:02:25 +0100 Subject: [Rtk-users] About Kaiser-Bessel Filter In-Reply-To: References: Message-ID: Yes! Try "-f CudaRayCast -b CudaVoxelBased". Simon On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang wrote: > Yes, thanks for your prompt reply. > what i want is to figure out how to set -f and -b to get i fastest > reconstruction (not -p,sorry for my mistake.). and in -b. which one is > related to our trilinear interpolation, CudaRayCast?? thanks > Best > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-19 16:40 GMT+03:00 Simon Rit : > >> Hi, >> I think you are looking at the code generated by gengetopt for the >> rtksart application. In general, it's simpler to simply do "rtksart --help" >> when you want to find out how to use a parameter. You will then find the >> following help section >> Projectors: >> -f, --fp=ENUM Forward projection method (possible >> values="Joseph", "RayCastInterpolator", >> "CudaRayCast" default=`Joseph') >> -b, --bp=ENUM Back projection method (possible >> values="VoxelBasedBackProjection", >> "Joseph", >> "CudaVoxelBased", "NormalizedJoseph" >> default=`VoxelBasedBackProjection') >> That should answer your question rtksart -b CudaVoxelBased. -p is the >> option for the path where the program will look for your projection images. >> Simon >> >> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang < >> guangming.zang at kaust.edu.sa> wrote: >> >>> Hi,Simon and Chao, >>> i want to test the cuda performance in SART algorithm. >>> but when i looked in the parameters in forwardprojection and >>> backprojection. i got the enum: >>> >>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0, >>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast }; >>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0, >>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph }; >>> >>> So if i want to use the trilinear intrtpolation forwardprojection you >>> mentioned , how should i set the -b and -p in SART? or how to choose -b and >>> -p that i can get a fastest reconstruction in SART in this case?? >>> >>> thanks for your help in advance. >>> Best >>> Guangming >>> >>> *Guangming Zang (Alex)* >>> *King Abdullah University of Science and Technology(KAUST)* >>> *University of Chinese Academy of Sciences(UCAS)* >>> >>> >>> 2014-11-18 19:47 GMT+03:00 Simon Rit : >>> >>>> The trilinear version is available with CUDA: >>>> >>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html >>>> Simon >>>> >>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang < >>>> guangming.zang at kaust.edu.sa> wrote: >>>> >>>>> Hi Chao, >>>>> Thanks very much for your prompt and so kind reply. >>>>> I will recheck the process of setting carefully with your suggestions >>>>> and a short report may be given later. >>>>> BTW, do you have any plan recently to add other interpolation >>>>> filter(e.g.Kaiser-Bessel or Trilinear)?? >>>>> Thanks for your time. >>>>> Regards >>>>> Guangming >>>>> >>>>> >>>>> >>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu : >>>>> >>>>>> Hi Guangming, >>>>>> >>>>>> To reconstruct a volume from a series of tiff files you have to let >>>>>> the algorithm know the geometrical relationship among the source, the >>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK >>>>>> uses projection matrices and image coordinates to understand the >>>>>> positioning of those projections. The projection matrices are based on a >>>>>> lot of geometrical parameters like gantry angle, source position, detector >>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I >>>>>> won't go though all since most of them have no differences if you use tiff >>>>>> files or whatever format as input. I focus on some tiff tips. >>>>>> >>>>>> In the simplest situation, the tiff files contain correct resolution >>>>>> (DPI) information, then you need to do nothing on these files. You have to >>>>>> specify the correct detector offset though, since in the tiff image >>>>>> coordinates the origin is the first pixel (corner pixel) which is >>>>>> apparently not the intersection of the central ray and the detector. The >>>>>> detector offsets in x and y actually mean the position of the image origin >>>>>> (the first pixel) in the coordinate system centred at the intersection. >>>>>> Since the direction cosines is an identity matrix and pixel sizes are >>>>>> positive, the detector offsets in x and y will be negative. >>>>>> >>>>>> If the resolution information of the tiff files is not correct, you >>>>>> have to rewrite this information. You can of course perform a >>>>>> pre-processing to change the DPI of all tiff files with a third-party >>>>>> software, or you can alter the RTK code to allow such changes after reading >>>>>> the images, by using a itk::ChangeInformationImageFilter filter. >>>>>> >>>>>> Another non-geometrical issue with tiff files is that when their >>>>>> integer pixel values are converted into attenuation, the maximum possible >>>>>> integer is used as the reference value. This may not be correct in >>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no >>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical >>>>>> fluctuation. If for instance you only use the lower 14 bits for your data >>>>>> then this problem is more severe. For sure you can correct this by changing >>>>>> the code and specify the correct reference value. >>>>>> >>>>>> Hope these can help. >>>>>> >>>>>> Regards, >>>>>> Chao >>>>>> >>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang < >>>>>> guangming.zang at kaust.edu.sa>: >>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> *Guangming Zang (Alex)* >>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>> >>>>>>> >>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang < >>>>>>> guangming.zang at kaust.edu.sa>: >>>>>>> >>>>>>>> Hi, >>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for >>>>>>>> your great work. >>>>>>>> and i was wondering do you have any plan to add other filters >>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here >>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf) >>>>>>>> BTW, i have read the messages sent by other users( >>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html >>>>>>>> ) >>>>>>>> but i still can not make it. can u help me and explain again about >>>>>>>> using a series of .tiff images ans sart algorithms to get the volume. >>>>>>>> Thanks in advance >>>>>>>> Best >>>>>>>> *King Abdullah University of Science and Technology(KAUST)* >>>>>>>> *University of Chinese Academy of Sciences(UCAS)* >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> This message and its contents, including attachments are intended >>>>>>> solely for the original recipient. If you are not the intended recipient or >>>>>>> have received this message in error, please notify me immediately and >>>>>>> delete this message from your computer system. Any unauthorized use or >>>>>>> distribution is prohibited. Please consider the environment before printing >>>>>>> this email. >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> ------------------------------ >>>>> This message and its contents, including attachments are intended >>>>> solely for the original recipient. If you are not the intended recipient or >>>>> have received this message in error, please notify me immediately and >>>>> delete this message from your computer system. Any unauthorized use or >>>>> distribution is prohibited. Please consider the environment before printing >>>>> this email. >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>> >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 06:21:56 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 14:21:56 +0300 Subject: [Rtk-users] some bugs in SART when running Reconstruction of Elekta Data Message-ID: Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 07:08:13 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 15:08:13 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: BTW, the Varian reconstruction has the same situation.I tested just now that fdk work well while sart not. Best Guangming ---------- Forwarded message ---------- From: Guangming Zang Date: 2014-11-20 14:21 GMT+03:00 Subject: some bugs in SART when running Reconstruction of Elekta Data To: "rtk-users at public.kitware.com" Hi, i ran the Reconstruction of Elekta Data example in wiki (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) when i use fdk to reconstruct the data, it work very well(can see the slice). When ran the SART algorithm, however,i got the result with same size of fdk algorithm's , but nothing can been seen in the slice. Here is the command i used: fdk: rtkfdk --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 SART(with different -f -b): rtksart --geometry elektaGeometry --path img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin -127.875,29.5,-127.875 the results are the same, can not see anything. Can you help me to figure it out or give me some suggestions? Thanks for your time. -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Thu Nov 20 09:02:02 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 20 Nov 2014 15:02:02 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: Message-ID: <546DF45A.2030806@creatis.insa-lyon.fr> Hi Guangming, I have just tested your command line and obtained some result, although it is indeed disappointing. SART generates strong artifacts on the borders of the image because some rays intersect only a few voxels on the borders and make the convergence very unstable. These artifacts are intense, so they mess up with the automatic choice of the window and level of the viewer. My advice : - Use "VV, the 4D slicer" to open your data (you should not see much at the beginning), and in the top right viewing pane, click in the center and hit the 'w' key. It will look at the pixels around the one you clicked, and adjust the window / level accordingly. Then you should see the reconstruction and the artifacts at the borders. Any other viewer with this "local windowing" option should do fine. - If you want to reconstruct a full volume, not just one slice, you can use SART : the artefacts on the borders should be much less intense once your whole object is in the reconstructed volume - If you want to reconstruct a single slice, or a few slices, use "rtkconjugategradient" instead. It does essentially the same as SART, but has a way steadier (although a bit slower) convergence. You can run it with the same options as SART, so all you have to do is replace "rtksart" by "rtkconjugategradient" in your command line examples (in particular, it runs fine on CUDA) Do not hesitate to ask if you happen to have more questions. Regards, Cyril On 11/20/2014 01:08 PM, Guangming Zang wrote: > BTW, the Varian reconstruction has the same situation.I tested just > now that fdk work well while sart not. > > Best > Guangming > */ > /* > > > ---------- Forwarded message ---------- > From: *Guangming Zang* > > Date: 2014-11-20 14:21 GMT+03:00 > Subject: some bugs in SART when running Reconstruction of Elekta Data > To: "rtk-users at public.kitware.com > " > > > > Hi, > i ran the Reconstruction of Elekta Data example in wiki > (http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction) > when i use fdk to reconstruct the data, it work very well(can see the > slice). When ran the SART algorithm, however,i got the result with > same size of fdk algorithm's , but nothing can been seen in the slice. > Here is the command i used: > fdk: > rtkfdk --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.5.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > SART(with different -f -b): > rtksart --geometry elektaGeometry --path > img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his --output > slice29.6.mha --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 > --origin -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f CudaRayCast -b CudaVoxelBased -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice_cuda.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > > rtksart -g elektaGeometry -f Joseph -b NormalizedJoseph -t 1 -p > img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o slice.mha > --spacing 0.25,0.25,0.25 --dimension 1024,1,1024 --origin > -127.875,29.5,-127.875 > the results are the same, can not see anything. > > Can you help me to figure it out or give me some suggestions? > Thanks for your time. > */ > /* > > > > ------------------------------------------------------------------------ > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 14:28:46 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Thu, 20 Nov 2014 22:28:46 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: <546DF45A.2030806@creatis.insa-lyon.fr> References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Cyril, It is so nice of you, thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes, actually, i want to use SART to reconstruct a whole volume. Considering that it may be kind of time-consuming, so i just try to reconstruct one slice first. And I want to use sart reconstruction algorithm from a series of projections data scanned from Nikon XT H 225 (.tif format,360 projections and 360 arcs) . But when using sart, I am not sure about the geometry in our RTK setting. File attached(two files) are the geometry information of object scanned and 360 projections, I used the command below, but I can not get the correct answer, I think it is because my geometry? setting is not correct, I used 2 commands: Command 1 rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 command 2 rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension 150 150 100 In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, does it mean that the coordination of scanned object?s center map to the projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) And in sart options , I do not know how to set origin in my case. So I just use defult value, but I think in my case, I should change the value. in the xml file, i think maybe this may related to the origin setting 21 1757 108 1851 293 1135 So can you help me to figure it out?? And , another question is, if I want to resize the projections(e.g, from 2000*2000 to 500*500. How should I change my geometry setting in this case)??? Again, thanks and very grateful for your any help and suggestion. I am not sure if you can see the attached file, so if you want, the 360 projections and geometry data are available at https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing The geometry only https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing Thanks for you all, Cyril ,Simon and Chao Best regards Guangming -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.ctprofile.xml Type: text/xml Size: 1882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VCC_toy_2014_11_20.xtekct Type: application/octet-stream Size: 949 bytes Desc: not available URL: From wuchao04 at gmail.com Thu Nov 20 18:14:01 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 00:14:01 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm. Before anything, first check the resolution of your tiff files and see if it is 200 dpi. Then try these geometry settings: rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 or rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 Then for reconstruction: rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800 No idea if these will work though... Best regards, Chao 2014-11-20 20:28 GMT+01:00 Guangming Zang : > Hi Cyril, > > It is so nice of you, thanks for your very helpful help and reply. And > thanks for introduction about the visualization tool ( VV ) . Yes, > actually, i want to use SART to reconstruct a whole volume. Considering > that it may be kind of time-consuming, so i just try to reconstruct one > slice first. > > And I want to use sart reconstruction algorithm from a series of > projections data scanned from Nikon XT H 225 (.tif format,360 > projections and 360 arcs) . But when using sart, I am not sure about the > geometry in our RTK setting. > > File attached(two files) are the geometry information of object scanned > and 360 projections, I used the command below, but I can not get the > correct answer, I think it is because my geometry? setting is not correct, > I used 2 commands: > > Command 1 > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 > > command 2 > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension 150 150 100 > > In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, > does it mean that the coordination of scanned object?s center map to the > projection? i used (0,-195) because in the geometry file (xml attached) the > object coordination is(0,192,633.82) And the spacing setting as the > VoxelSize of x ,y,z. which is 0.07988 in xml. > > In command 2 , I am not sure about the dimension and origin setting. I > setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, > VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) > > And in sart options , I do not know how to set origin in my case. So I > just use defult value, but I think in my case, I should change the value. > > in the xml file, i think maybe this may related to the origin setting > > > > 21 > > 1757 > > 108 > > 1851 > > 293 > > 1135 > > > > So can you help me to figure it out?? > > And , another question is, if I want to resize the projections(e.g, from > 2000*2000 to 500*500. How should I change my geometry setting in this > case)??? > > Again, thanks and very grateful for your any help and suggestion. > > I am not sure if you can see the attached file, so if you want, the 360 > projections and geometry data are available at > https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing > > The geometry only > > > https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing > > > Thanks for you all, Cyril ,Simon and Chao > > > Best regards > > Guangming > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:40:20 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:40:20 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Dear Chao, thanks very much for your help. I will try this command now. Result will be given later. Thanks again for your generous help and valuable time. Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? BTW? as for the xtekct file, file attached is the geometry of Nikon H225 in the lab . [image: ???? 1] Best regards /???? Guangming. *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:14 GMT+03:00 Chao Wu : > Without more details I can only guess the meanings in your device xtekct > file... suppose that the unit is mm. > > Before anything, first check the resolution of your tiff files and see if > it is 200 dpi. > > Then try these geometry settings: > > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > or > rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 > --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 > > Then for reconstruction: > > rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p > C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 > --spacing=0.08 --dimension=1800,900,1800 > > No idea if these will work though... > > Best regards, > Chao > > > 2014-11-20 20:28 GMT+01:00 Guangming Zang : > >> Hi Cyril, >> >> It is so nice of you, thanks for your very helpful help and reply. And >> thanks for introduction about the visualization tool ( VV ) . Yes, >> actually, i want to use SART to reconstruct a whole volume. Considering >> that it may be kind of time-consuming, so i just try to reconstruct one >> slice first. >> >> And I want to use sart reconstruction algorithm from a series of >> projections data scanned from Nikon XT H 225 (.tif format,360 >> projections and 360 arcs) . But when using sart, I am not sure about the >> geometry in our RTK setting. >> >> File attached(two files) are the geometry information of object scanned >> and 360 projections, I used the command below, but I can not get the >> correct answer, I think it is because my geometry? setting is not correct, >> I used 2 commands: >> >> Command 1 >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >> >> command 2 >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension 150 150 100 >> >> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >> does it mean that the coordination of scanned object?s center map to the >> projection? i used (0,-195) because in the geometry file (xml attached) the >> object coordination is(0,192,633.82) And the spacing setting as the >> VoxelSize of x ,y,z. which is 0.07988 in xml. >> >> In command 2 , I am not sure about the dimension and origin setting. I >> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >> >> And in sart options , I do not know how to set origin in my case. So I >> just use defult value, but I think in my case, I should change the value. >> >> in the xml file, i think maybe this may related to the origin setting >> >> >> >> 21 >> >> 1757 >> >> 108 >> >> 1851 >> >> 293 >> >> 1135 >> >> >> >> So can you help me to figure it out?? >> >> And , another question is, if I want to resize the projections(e.g, from >> 2000*2000 to 500*500. How should I change my geometry setting in this >> case)??? >> >> Again, thanks and very grateful for your any help and suggestion. >> >> I am not sure if you can see the attached file, so if you want, the 360 >> projections and geometry data are available at >> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >> >> The geometry only >> >> >> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >> >> >> Thanks for you all, Cyril ,Simon and Chao >> >> >> Best regards >> >> Guangming >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MCT225-Features.jpg Type: image/jpeg Size: 97621 bytes Desc: not available URL: From guangming.zang at kaust.edu.sa Thu Nov 20 18:49:01 2014 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 21 Nov 2014 02:49:01 +0300 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: Hi Chao, I checked the tif file and just found the file information like this: Horizontal resolution 300 dpi Vertical resolution 300 dpi dimensions 1916*1536 bit depth 16 So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi??? Best Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2014-11-21 2:40 GMT+03:00 Guangming Zang : > Dear Chao, > thanks very much for your help. > I will try this command now. Result will be given later. > Thanks again for your generous help and valuable time. > Another question is , how to visual the large volume effectively?? 3D > slicer is okay to handle this?? > BTW? as for the xtekct file, file attached is the geometry of Nikon > H225 in the lab . > [image: ???? 1] > > Best regards /???? > Guangming. > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:14 GMT+03:00 Chao Wu : > >> Without more details I can only guess the meanings in your device xtekct >> file... suppose that the unit is mm. >> >> Before anything, first check the resolution of your tiff files and see if >> it is 200 dpi. >> >> Then try these geometry settings: >> >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> or >> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >> >> Then for reconstruction: >> >> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >> --spacing=0.08 --dimension=1800,900,1800 >> >> No idea if these will work though... >> >> Best regards, >> Chao >> >> >> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >> >>> Hi Cyril, >>> >>> It is so nice of you, thanks for your very helpful help and reply. And >>> thanks for introduction about the visualization tool ( VV ) . Yes, >>> actually, i want to use SART to reconstruct a whole volume. Considering >>> that it may be kind of time-consuming, so i just try to reconstruct one >>> slice first. >>> >>> And I want to use sart reconstruction algorithm from a series of >>> projections data scanned from Nikon XT H 225 (.tif format,360 >>> projections and 360 arcs) . But when using sart, I am not sure about the >>> geometry in our RTK setting. >>> >>> File attached(two files) are the geometry information of object scanned >>> and 360 projections, I used the command below, but I can not get the >>> correct answer, I think it is because my geometry? setting is not correct, >>> I used 2 commands: >>> >>> Command 1 >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>> >>> command 2 >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension 150 150 100 >>> >>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting, >>> does it mean that the coordination of scanned object?s center map to the >>> projection? i used (0,-195) because in the geometry file (xml attached) the >>> object coordination is(0,192,633.82) And the spacing setting as the >>> VoxelSize of x ,y,z. which is 0.07988 in xml. >>> >>> In command 2 , I am not sure about the dimension and origin setting. I >>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>> >>> And in sart options , I do not know how to set origin in my case. So I >>> just use defult value, but I think in my case, I should change the value. >>> >>> in the xml file, i think maybe this may related to the origin setting >>> >>> >>> >>> 21 >>> >>> 1757 >>> >>> 108 >>> >>> 1851 >>> >>> 293 >>> >>> 1135 >>> >>> >>> >>> So can you help me to figure it out?? >>> >>> And , another question is, if I want to resize the projections(e.g, from >>> 2000*2000 to 500*500. How should I change my geometry setting in this >>> case)??? >>> >>> Again, thanks and very grateful for your any help and suggestion. >>> >>> I am not sure if you can see the attached file, so if you want, the 360 >>> projections and geometry data are available at >>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>> >>> The geometry only >>> >>> >>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>> >>> >>> Thanks for you all, Cyril ,Simon and Chao >>> >>> >>> Best regards >>> >>> Guangming >>> >>> ------------------------------ >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: From wuchao04 at gmail.com Fri Nov 21 02:08:17 2014 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 21 Nov 2014 08:08:17 +0100 Subject: [Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data In-Reply-To: References: <546DF45A.2030806@creatis.insa-lyon.fr> Message-ID: or scale you sdd by 2/3. Regards, Chao Sent from Samsung Galaxy Note 3 2014?11?21? 12:49 AM? "Guangming Zang" ??? > Hi Chao, > I checked the tif file and just found the file information like this: > Horizontal resolution 300 dpi > Vertical resolution 300 dpi > dimensions 1916*1536 > bit depth 16 > > So it means that before the reconstruction, i should use some tool to > convert the projections images from 300dpi to 200dpi??? > Best > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > 2014-11-21 2:40 GMT+03:00 Guangming Zang : > >> Dear Chao, >> thanks very much for your help. >> I will try this command now. Result will be given later. >> Thanks again for your generous help and valuable time. >> Another question is , how to visual the large volume effectively?? 3D >> slicer is okay to handle this?? >> BTW? as for the xtekct file, file attached is the geometry of Nikon >> H225 in the lab . >> [image: ???? 1] >> >> Best regards /???? >> Guangming. >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> 2014-11-21 2:14 GMT+03:00 Chao Wu : >> >>> Without more details I can only guess the meanings in your device xtekct >>> file... suppose that the unit is mm. >>> >>> Before anything, first check the resolution of your tiff files and see >>> if it is 200 dpi. >>> >>> Then try these geometry settings: >>> >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> or >>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 >>> --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536 >>> >>> Then for reconstruction: >>> >>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p >>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>> --spacing=0.08 --dimension=1800,900,1800 >>> >>> No idea if these will work though... >>> >>> Best regards, >>> Chao >>> >>> >>> 2014-11-20 20:28 GMT+01:00 Guangming Zang : >>> >>>> Hi Cyril, >>>> >>>> It is so nice of you, thanks for your very helpful help and reply. And >>>> thanks for introduction about the visualization tool ( VV ) . Yes, >>>> actually, i want to use SART to reconstruct a whole volume. Considering >>>> that it may be kind of time-consuming, so i just try to reconstruct one >>>> slice first. >>>> >>>> And I want to use sart reconstruction algorithm from a series of >>>> projections data scanned from Nikon XT H 225 (.tif format,360 >>>> projections and 360 arcs) . But when using sart, I am not sure about the >>>> geometry in our RTK setting. >>>> >>>> File attached(two files) are the geometry information of object >>>> scanned and 360 projections, I used the command below, but I can not get >>>> the correct answer, I think it is because my geometry? setting is not >>>> correct, I used 2 commands: >>>> >>>> Command 1 >>>> >>>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 >>>> --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195 >>>> >>>> command 2 >>>> >>>> rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 >>>> -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 >>>> --spacing=0.08 --dimension 150 150 100 >>>> >>>> In command 1, I am not sure about the proj_iso_x and proj_iso_y >>>> setting, does it mean that the coordination of scanned object?s center map >>>> to the projection? i used (0,-195) because in the geometry file (xml >>>> attached) the object coordination is(0,192,633.82) And the spacing >>>> setting as the VoxelSize of x ,y,z. which is 0.07988 in xml. >>>> >>>> In command 2 , I am not sure about the dimension and origin setting. I >>>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX, >>>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) >>>> >>>> And in sart options , I do not know how to set origin in my case. So I >>>> just use defult value, but I think in my case, I should change the value. >>>> >>>> in the xml file, i think maybe this may related to the origin setting >>>> >>>> >>>> >>>> 21 >>>> >>>> 1757 >>>> >>>> 108 >>>> >>>> 1851 >>>> >>>> 293 >>>> >>>> 1135 >>>> >>>> >>>> >>>> So can you help me to figure it out?? >>>> >>>> And , another question is, if I want to resize the projections(e.g, >>>> from 2000*2000 to 500*500. How should I change my geometry setting in this >>>> case)??? >>>> >>>> Again, thanks and very grateful for your any help and suggestion. >>>> >>>> I am not sure if you can see the attached file, so if you want, the 360 >>>> projections and geometry data are available at >>>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing >>>> >>>> The geometry only >>>> >>>> >>>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing >>>> >>>> >>>> Thanks for you all, Cyril ,Simon and Chao >>>> >>>> >>>> Best regards >>>> >>>> Guangming >>>> >>>> ------------------------------ >>>> This message and its contents, including attachments are intended >>>> solely for the original recipient. If you are not the intended recipient or >>>> have received this message in error, please notify me immediately and >>>> delete this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before printing >>>> this email. >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 258513 bytes Desc: not available URL: